cBioPortal validation report

Study directory:
./generated_data/mmrf_gdc

For details, please see the documentation on file formats supported by cBioPortal

cBioPortal version 6.0.2

Validation status: Failed
Line Number Column Number Message Value Encountered
Debug Requesting info from portal at 'https://www.cbioportal.org'
Debug Requesting cancer-types from portal at 'https://www.cbioportal.org'
Debug Requesting genes from portal at 'https://www.cbioportal.org'
Debug Requesting genesets from portal at 'https://www.cbioportal.org'
Debug Requesting genesets_version from portal at 'https://www.cbioportal.org'
Debug Requesting gene-panels from portal at 'https://www.cbioportal.org'
Error Cancer type of study is neither known to the portal nor defined in a cancer_type file
Debug Validating case lists
Info Validation of case list folder complete
Info Validation complete
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Error Multiple case lists with this stable_id defined in the study mmrf_gdc_all (already defined in meta_study.txt)
Line Number Column Number Message Value Encountered
Debug Starting validation of meta file
Info Validation of meta file complete
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Warning Columns DFS_MONTHS and/or DFS_STATUS not found. Disease free analysis feature will not be available for this study.
Info Validation of file complete
Info Read 1000 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Info Validation of file complete
Info Read 1145 lines. Lines with warning: 0. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Warning 87, 193, 194… Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1899 values
Info Validation of file complete
Info Read 40797 lines. Lines with warning: 1899. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Warning 87, 193, 194… Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1899 values
Info Validation of file complete
Info Read 40797 lines. Lines with warning: 1899. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Warning 87, 193, 194… Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1899 values
Info Validation of file complete
Info Read 40797 lines. Lines with warning: 1899. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Warning 87, 193, 194… Entrez gene id not known to the cBioPortal instance. This record will not be loaded. Might be new or deprecated Entrez gene id. 100033819, 100126296, 100126297… See all 1899 values
Info Validation of file complete
Info Read 40797 lines. Lines with warning: 1899. Lines with error: 0
Line Number Column Number Message Value Encountered
Debug Starting validation of file
Warning 3 Including the SWISSPROT column is recommended to make sure that the UniProt canonical isoform is used when drawing Pfam domains in the mutations view
Info 6, 7, 8… Line will not be loaded due to the variant classification filter. Filtered types: [Silent, Intron, 3'UTR, 3'Flank, 5'UTR, 5'Flank, IGR, RNA] 3'UTR, 5'UTR, 3'Flank… See all 94662 values